- BBClist - maillist.psb.ugent.be

vacancy teaching assistant UGent Global Campus Korea
by Willem Waegeman 22 Jun '17

22 Jun '17

Dear BBC-list, please find in attach a vacancy for a teaching assistant in the field of mathematical modelling of biochemical networks. This is under main supervision of Prof. Shodhan Rao at the UGent global campus in Korea. Feel free to distribute among interested students. -- Prof. dr. Willem Waegeman Research Unit Knowledge-Based Systems (KERMIT) Department of Mathematical Modelling, Statistics and Bioinformatics Coupure links 653 9000 Ghent, Belgium Phone: + 32 9 264 92 00 Skype: willem.waegeman www.kermit.ugent.be users.ugent.be/~wwaegemn

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vacancy omics data scientist at VITO Health
by Langie Sabine 20 Jun '17

20 Jun '17

Beste/Dear, VITO Health is looking for an R&D PROFESSIONAL HEALTH - OMICS DATA SCIENTIST: https://vito.taleo.net/careersection/jobdetail.ftl?job=1700001P&lang=nl The English version can be found her: https://vito.taleo.net/careersection/jobdetail.ftl?job=1700001P&lang=en VITO-Health Team [cid:image001.png@01D22B8F.46C6FF50]<http://vito.be/> [cid:image003.png@01D22B8F.46C6FF50]<https://www.facebook.com/VITObelgium> [cid:image004.png@01D22B8F.46C6FF50]<https://twitter.com/VITObelgium> [cid:image005.png@01D22B8F.46C6FF50]<https://www.linkedin.com/company/vito> [cid:image006.png@01D22B8F.46C6FF50]<https://vimeo.com/vitovideo> VITO Disclaimer: http://www.vito.be/e-maildisclaimer

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Course Applied Microbial Genomics training
by Bruggen Martijn van der 19 Jun '17

19 Jun '17

Dear all, At HAN BioCentre we organize the course "Applied Microbial Genomics" More information can be found at: https://www.han.nl/opleidingen/exchange-courses/applied-microbial-genomics/ Kind regards, Martijn. Drs. M.H.H. van der Bruggen Docent bioinformatica / Opleidingscoördinator bioinformatica HAN University of Applied Sciences Institute of Applied Sciences (www.han.nl/appliedsciences) Postal address: P.O. Box 6960 | 6503 GL NIJMEGEN | The Netherlands | Martijn.vanderBruggen(a)han.nl<mailto:Martijn.vanderBruggen@han.nl> Visiting Address: Laan van Scheut 2 | Room 0.06 | 6525 EM NIJMEGEN | The Netherlands | +31-6-55206344 Present: Monday - Tuesday - Wednesday - Thursday - Friday [untitled]

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Data Manipulation and Visualisation with Python 10-14 July 2017 & GATK Best Practices for Variant Discovery 17-19 July 2017 - Few places left
by Bert Overduin 16 Jun '17

16 Jun '17

Dear all, We have very few places left on the following workshops (first come, first served). With kind regards, Bert ************************* DATA MANIPULATION AND VISUALISATION WITH PYTHON One of the strengths of the Python language is the availability of mature, high-quality libraries for working with scientific data. Integration between the most popular libraries has lead to the concept of a "scientific Python stack": a collection of packages which are designed to work well together. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. DATE: Monday 10 – Friday 14 July 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 26 June 2017 noon CANCELLATION DEADLINE: Monday 3 July 2017 noon PLACES: 20 (first come, first served) REGISTRATION FEE: £525 (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) Martin Jones ( martin(a)pythonforbiologists.com) FOR MORE DETAILS AND TO REGISTER: http://genomics.ed.ac.uk/servi ces/data-manipulation-and-visualisation-python ************************* GATK BEST PRACTICES FOR VARIANT DISCOVERY This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq-specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. DATE: Monday 17 - Wednesday 19 July 2017 VENUE: The King's Buildings,The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 3 July 2017 CANCELLATION DEADLINE: Monday 10 July 2017 PLACES: 85 (lectures), 30 (hands-on sessions) (first come, first served) REGISTRATION FEE: £70 for the lectures, £35 for each half-day hands-on session (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) FOR MORE DETAILS AND TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best-practices-variant-discovery ************************ -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Vacancy : Software Developer
by Vandeweyer Geert 15 Jun '17

15 Jun '17

The Centre of Medical Genetics at the University of Antwerp has a vacancy for a Software Developer. For more information, see attachment or https://www.uantwerpen.be/en/jobs/vacancies/ap/2017bapffbdef189/ Best regards, Geert Vandeweyer -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43/6 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)uantwerpen.be https://www.uantwerpen.be/en/rg/cognet/ http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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small molecule bioinformatics software developer position at UAntwerpen
by Laukens Kris 14 Jun '17

14 Jun '17

Dear colleagues, feel free to distribute this vacancy within your network. Thank you. Kind regards, Kris Laukens The Faculty of Sciences of the University of Antwerp is seeking to fill the following full-time vacancy in the Department of Mathematics and Computer Science. Scientific software developer in the field of pharma data analytics. This project will be conducted at the interface of 1) the biodata mining team (under supervision of prof. Kris Laukens), a rapidly growing, multi-disciplinary unit within the ADReM data lab / biomina of the department of Mathematics and Computer Science (University of Antwerp, Belgium); 2) (under supervision of prof. Dirk Valkenborg) the Center for Statistics (University of Hasselt, Belgium); and 3) a major pharmaceutical industry partner. Job description You will develop novel implementations for cutting-edge data mining and machine learning approaches, tailored towards the field of small molecule mass-spectrometry. This chemical field plays a central role in many top-notch pharmaceutical and biotechnological applications. Its enormous data complexity requires novel, robust data processing, management and visualisation techniques. As a scientific programmer, you will fulfill a central role in translating the newest data science approaches to industry-grade applications. While being familiar with the type of data and applications is not a prerequisite, you will work closely with domain experts to understand the data and its particular problems, and you will learn to understand the challenges of their applicability in a real laboratory setting. You will implement your methods in a user-friendly software environment and application-programming interface. You collaborate with academic researchers in different disciplines (from computational sciences to life sciences) within the consortium (biomina- the biomedical informatics network Antwerpen, UAntwerpen, UHasselt) and with the industrial partners of the project. Profile and requirements • You have a master or doctoral degree in computer science (data science, software engineering, ...), bioinformatics or chemoinformatics; • You have a good understanding of data mining, statistics, machine learning and visualisation techniques. • You have excellent (scientific) software and database development skills. • You have a strong interest in translating the newest data science solutions to industry-grade applications. • You have excellent interdisciplinary English communication skills, you are quality-oriented and creative, and eager to emerge in new domains. Proven project management skills and industrial experience are a plus; • Previous experience in data mining for bioinformatics, mass spectrometry or related techniques is an advantage but not a prerequisite; We offer • A software developer or postdoctoral position (depending on your degree) for a period of two years. The default start date of the position is November 1st 2017 (but this is open for negotiation); • A salary commensurate with your experience and qualifications; • A dynamic, stimulating and multinational work environment. Interested? Candidates are invited to send a motivation letter, a detailed CV and contact info of at least two references (including email addresses and phone numbers) to Prof. Kris Laukens (kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be>) and Prof. Dirk Valkenborg (dirk.valkenborg(a)uhasselt.be<mailto:dirk.valkenborg@uhasselt.be>). Don’t hesitate to contact us in advance for more information. -- Kris Laukens, PhD Associate professor bioinformatics - biodata mining Advanced Database Research and Modelling (ADReM) Biomedical Informatics Network Antwerpen (biomina) Department of Mathematics and Computer Science University of Antwerp Middelheimlaan 1, G.111 B-2020 Antwerpen, Belgium T +32 (0)3 265 33 10 E kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be> W www.uantwerpen.be/en/staff/kris-laukens/<http://www.uantwerpen.be/en/staff/kris-laukens/>

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BioSB Course Quantitative and Predictive Modelling, 26-30 June 2017 in Wageningen, the Netherlands
by Celia van Gelder 11 Jun '17

11 Jun '17

BioSB Course Quantitative and Predictive Modelling Date: 26-30 June, 2017 Location: Wageningen Course Coordinators: Natal van Riel (TUE) & Jaap Molenaar (WUR) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Please note that this course is free of charge for PhDs who are or become a <http://biosb.nl/about/members/biosb-membership-information/> member of the BioSB research school. Description On June 26-30 2017, BioSB organises the second edition of the course Quantitative and Predictive Modelling (QPM). In this course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques and aims as such at a broad audience. The course is a mixture of theory sessions and computer practicals. During the practicals most of the time Matlab will be used. Participants not acquainted with Matlab will get an introduction. The course has to be completed with assignments in the form of practical exercises as homework afterwards. Target audience and learning objectives This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from the private sector are also welcome. Participants are expected to have some experience in modelling with differential equations. The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling, parameter estimation and uncertainty analysis. In the course the students will learn: * How to set-up a dynamic model to represent biological networks using different interaction mechanisms * To implement, simulate and analyse dynamic network models in different software tools * To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes * To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions This course is part of the <http://biosb.nl/education/course-portfolio-2/> Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/> . Beste regards, Femke Francissen Femke Francissen Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: <mailto:femke.francissen@biosb.nl> femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn <http://nl.linkedin.com/in/femkefrancissen> link <http://www.dtls.nl/wp-content/uploads/2014/09/BioSB_logo_full_250x226.jpg>

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Vacancy Bioinformatics and Data Science Trainer ELIXIR-Belgium
by Alexander Botzki 10 Jun '17

10 Jun '17

Dear all, At the VIB Bioinformatics Core, we recently opened one position for a bioinformatics and data science trainer: ELIXIR Trainer at VIB Bioinformatics Core http://www.vib.be/en/jobs/Pages/Bioinformatics-and-Data-Science-Trainer-ELI… Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Bioinformatics position at the Princess Maxima Center for Pediatric Oncology
by Patrick Kemmeren 09 Jun '17

09 Jun '17

Dear all, Within the Princess Maxima Center for Pediatric Oncology, we currently have an open vacancy for a Bioinformatician (PhD or Msc)! For more information, please see: http://www.werkenbijprinsesmaximacentrum.nl/vacaturetekst-engels/scientist-… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator T +31 (0)88 972 55 05 | M +31 (0)6 53 11 25 53 Princess Maxima Center * * *Princess Máxima Center for Pediatric Oncology* *Location Hubrecht institute*| Uppsalalaan 8 | 3584 CT Utrecht | T +31 (0)88 972 90 00 |***> Website* <http://prinsesmaximacentrum.com/>

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Galaxy Community Conference: Register by 16 June
by Dave Clements 08 Jun '17

08 Jun '17

2017 Galaxy Community Conference (GCC2017) 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ https://gcc2017.sched.com/ -- The Galaxy Community Conference (GCC) <https://gcc2017.sciencesconf.org/> brings together researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and features two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups <https://gcc2017.sched.com/overview/type/Conference>, all about data-intensive biology and the tools that support it. GCC2017 also features data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just 10km from the Mediterranean. Registration closes 16 June <https://gcc2017.sciencesconf.org/page/registration>. Costs start at 75€ per day for postdocs and students. If you work in data intensive life science research then GCC2017 is an ideal opportunity to present your work. Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather <https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m…> submission are still open, and there is limited space available for late poster and computer demo submissions <https://gcc2017.sciencesconf.org/page/submit>. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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